BN1585 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 1.0886e-04 5.1343e-02
Layer 4 3.2868e-04 2.1801e-03
Layer 5 5.5928e-04 2.8042e-03
Layer 6 1.5066e-03 7.7405e-03
Layer 2 3.5140e-03 6.8675e-02
WM 2.0565e-02 1.0112e-01
Layer 1 6.4937e-01 6.7310e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 6 2.3154 0.7281
NUDT4 Layer 5 2.2520 0.6235
CPLX1 Layer 5 2.5566 0.6215
PNMA2 Layer 5 2.2461 0.6159
TUBB2A Layer 5 2.3105 0.6107
NRN1 Layer 4 2.5332 0.6060
STMN2 Layer 5 2.5215 0.6037
SNRPN Layer 4 2.3438 0.5992
NDRG4 Layer 5 2.4639 0.5909
SYN2 Layer 5 2.7480 0.5907
SH3GL2 Layer 5 2.2422 0.5894
TLE5 Layer 5 2.1973 0.5836
PJA2 Layer 5 2.2070 0.5811
ENO2 Layer 5 2.3809 0.5787
MLLT11 Layer 5 2.4180 0.5780
BSCL2 Layer 5 2.2363 0.5767
BASP1 Layer 5 2.1680 0.5763
ATP6V1B2 Layer 5 2.2266 0.5702
RGS4 Layer 6 2.2578 0.5702
BMERB1 Layer 5 2.2773 0.5700
TAGLN3 Layer 6 2.2969 0.5696
DCLK1 Layer 5 2.1562 0.5685
STX1B Layer 4 2.3027 0.5643
LMO4 Layer 4 2.3965 0.5631
TOLLIP Layer 5 2.2715 0.5587
MTPN Layer 5 2.0723 0.5585
CAPNS1 Layer 5 2.0723 0.5584
ATP6V1A Layer 5 2.2715 0.5583
NAPB Layer 5 2.2441 0.5570
SYNGR3 Layer 5 1.9580 0.5565
SV2A Layer 5 2.2803 0.5565
SLC25A22 Layer 5 2.0957 0.5560
PLEKHB2 Layer 4 2.1719 0.5556
CEND1 Layer 5 2.1816 0.5548
NRSN1 Layer 5 2.3340 0.5547
SYT4 Layer 4 2.2197 0.5542
DYNLRB1 Layer 5 2.0625 0.5538
SNCB Layer 4 2.3594 0.5529
FAM49A Layer 5 2.0684 0.5522
MGST3 Layer 5 2.3496 0.5518
ARHGDIG Layer 6 2.1250 0.5499
SARAF Layer 5 2.2422 0.5497
GAP43 Layer 3 2.2617 0.5478
OAZ1 Layer 5 2.2773 0.5474
BSN Layer 6 2.1387 0.5459
PI4KA Layer 6 2.3125 0.5452
NUAK1 Layer 4 2.2070 0.5443
EPDR1 Layer 5 2.0547 0.5441
NCALD Layer 5 2.3574 0.5440
STMN1 Layer 5 2.1094 0.5437

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1585
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1585_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1585/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1585/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1585/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1585/report/PD/BN1585_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1585/report/PD/BN1585_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 05:25:33
  • Number of Processes: 10
  • Spending Time: 0h 3m